SMTL ID : 1d7u.1

Crystal structure of the complex of 2,2-dialkylglycine decarboxylase with LCS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

4 x NA: SODIUM ION(Non-functional Binders)

NA.1: 5 residues within 4Å: Chain A: A.95, T.98, P.99, P.100, L.102 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.98, A:L.102 NA.4: 5 residues within 4Å: Chain B: A.95, T.98, P.99, P.100, L.102 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.98, B:T.98 NA.7: 5 residues within 4Å: Chain C: A.95, T.98, P.99, P.100, L.102 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.98 NA.10: 5 residues within 4Å: Chain D: A.95, T.98, P.99, P.100, L.102 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.98

4 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain A: L.78, S.80, T.303, H.304, V.305, D.307 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.78, A:S.80, A:T.303, A:D.307, H2O.2 K.5: 6 residues within 4Å: Chain B: L.78, S.80, T.303, H.304, V.305, D.307 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:L.78, B:S.80, B:T.303, B:D.307, H2O.7 K.8: 6 residues within 4Å: Chain C: L.78, S.80, T.303, H.304, V.305, D.307 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:L.78, C:S.80, C:T.303, C:D.307, H2O.13 K.11: 6 residues within 4Å: Chain D: L.78, S.80, T.303, H.304, V.305, D.307 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:L.78, D:S.80, D:T.303, D:D.307, H2O.19

4 x LCS: [5-hydroxy-6-methyl-4-({[(4E)-3-oxo-1,2-oxazolidin-4-ylidene]amino}methyl)pyridin-3-yl]methyl dihydrogen phosphate(Non-covalent)

LCS.3: 18 residues within 4Å: Chain A: Q.52, T.110, G.111, A.112, N.115, W.138, H.139, G.140, E.210, S.215, D.243, A.245, Q.246, K.272, R.406 Chain C: Y.301, T.302, T.303 19 PLIP interactions: 14 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:E.210, A:A.245 Hydrogen bonds: A:Q.52, A:T.110, A:G.111, A:A.112, A:N.115, A:Q.246, A:K.272, A:R.406, A:R.406, C:T.303, C:T.303 Water bridges: A:W.138, A:E.210, A:S.271, C:Y.301, C:T.303, C:T.303 LCS.6: 18 residues within 4Å: Chain B: Q.52, T.110, G.111, A.112, N.115, W.138, H.139, G.140, E.210, S.215, D.243, A.245, Q.246, K.272, R.406 Chain D: Y.301, T.302, T.303 19 PLIP interactions: 14 interactions with chain B, 5 interactions with chain D Hydrophobic interactions: B:E.210, B:A.245 Hydrogen bonds: B:Q.52, B:T.110, B:G.111, B:A.112, B:N.115, B:Q.246, B:K.272, B:R.406, B:R.406, D:T.303, D:T.303 Water bridges: B:W.138, B:E.210, B:S.271, D:Y.301, D:T.303, D:T.303 LCS.9: 18 residues within 4Å: Chain A: Y.301, T.302, T.303 Chain C: Q.52, T.110, G.111, A.112, N.115, W.138, H.139, G.140, E.210, S.215, D.243, A.245, Q.246, K.272, R.406 18 PLIP interactions: 14 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:E.210, C:A.245 Hydrogen bonds: C:Q.52, C:G.111, C:A.112, C:N.115, C:Q.246, C:K.272, C:R.406, C:R.406, A:T.303, A:T.303, A:T.303 Water bridges: C:T.110, C:W.138, C:E.210, C:S.271, A:T.302 LCS.12: 18 residues within 4Å: Chain B: Y.301, T.302, T.303 Chain D: Q.52, T.110, G.111, A.112, N.115, W.138, H.139, G.140, E.210, S.215, D.243, A.245, Q.246, K.272, R.406 18 PLIP interactions: 14 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: D:E.210, D:A.245 Hydrogen bonds: D:Q.52, D:G.111, D:A.112, D:N.115, D:Q.246, D:K.272, D:R.406, D:R.406, B:T.303, B:T.303, B:T.303 Water bridges: D:T.110, D:W.138, D:E.210, D:S.271, B:T.302

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malashkevich, V.N. et al., Crystal structures of dialkylglycine decarboxylase inhibitor complexes. J.Mol.Biol. (1999)

Release Date

1999-11-19

Peptides

PROTEIN (2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE)): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

PROTEIN (2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE))

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